April 2020 - Neurofedora - Fedora mailing-lists

Announcing the release of the CompNeuro-Fedora OS for Computational Neuroscientists
by Ankur Sinha 28 Apr '20

28 Apr '20

Hello everyone, This is the e-mail I've sent out to various neuroscience mailing lists. Please spread the word. Thank you all, for all your work. I hope we can continue our work and keep bringing our Free/Open Source work to (Neuro)Science. 👏 ----- Hello everyone, (Apologies for the cross-posts) The NeuroFedora team is excited to announce the first release of the CompNeuro-Fedora operating system for computational neuroscientists. https://labs.fedoraproject.org/en/comp-neuro/ CompNeuro-Fedora is a Fedora Linux based Free/Open Source operating system that includes a plethora of tools for computational modelling. These tools are built from their sources as per the Fedora packaging guidelines that enforce the current best practices in software development. So, all you have to do is: - download the image, - install it to disk or a virtual machine (or run it "live"), and - get to work! This release of the ISO image is based on the popular GNOME desktop environment. For computational neuroscience, it includes: Auryn, Bionetgen, Calc: calcium-calculator, COPASI, GetDP, GENESIS, MOOSE, NEST simulator, NEURON, PyLEMS, Smoldyn; along with multiple tools used in analysis: the complete Python science stack: NumPy, SciPy, Matplotlib, IPython, SymPy, and Pandas, R, Julia, GNU Octave, GNUPlot, Paraview, and others. Apart from this set of tools, the NeuroFedora team also provides more neuroscience software that can be installed from the Fedora repositories. Additionally, you also have access to the *complete* set of Free/Open Source software packages available for the Fedora Linux distribution. You can read more about the CompNeuro-Fedora release here: https://neuroblog.fedoraproject.org/2020/04/28/fedora-32-computational-neur… NeuroFedora is a Free/Open Source volunteer community based initiative to support the use of Free/Open Source software in Neuroscience. The team consists wholly of volunteers who spend a few hours a week on this project. We would love to hear from you, and for you to join us. We, especially encourage students to join the community to develop their skills while contributing to NeuroFedora. You can learn more about NeuroFedora here: https://neuro.fedoraproject.org You can get in touch with the community using any of our communication channels: https://docs.fedoraproject.org/en-US/neurofedora/communicating/ -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Logs for the Open NeuroFedora Meeting: 1800 UTC on Monday, 28th April
by Aniket Pradhan 27 Apr '20

27 Apr '20

Hey there! Thanks, everyone for attending the meeting. We shall meet in two weeks' time, which is 12th May 2020, at 1800 UTC. Links to the logs from today's meeting: * https://meetbot.fedoraproject.org/fedora-neuro/2020-04-27/neurofedora.2020-… * https://meetbot.fedoraproject.org/fedora-neuro/2020-04-27/neurofedora.2020-… Minutes in text format for your convenience: ======================================= #fedora-neuro: NeuroFedora - 2020-04-27 ======================================= Meeting started by MeWjOr at 18:01:11 UTC. The full logs are available at https://meetbot.fedoraproject.org/fedora-neuro/2020-04-27/neurofedora.2020-… . Meeting summary --------------- * Agenda for today's meeting (MeWjOr, 18:02:30) * Intro/roll call (MeWjOr, 18:02:39) * Tasks from last meeting https://meetbot.fedoraproject.org/fedora-neuro/2020-04-07/neurofedora.2020-… (MeWjOr, 18:02:55) * Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… (MeWjOr, 18:03:09) * Bugzilla tickets https://tinyurl.com/neurofedora-bugs (MeWjOr, 18:03:26) * compose status (MeWjOr, 18:03:45) * (neuro)science query of the week (MeWjOr, 18:03:51) * Next meeting, time, date, chair (MeWjOr, 18:03:55) * Open floor (MeWjOr, 18:04:01) * Intros/Roll call (MeWjOr, 18:04:14) * @ankursinha: UTC+1, NeuroFedora, packaging, other misc bits (FranciscoD, 18:04:57) * Tasks from last meeting https://meetbot.fedoraproject.org/fedora-neuro/2020-04-07/neurofedora.2020-… (MeWjOr, 18:09:20) * (MeWjOr, 18:09:34) * FranciscoD Comment on the ticket to provide feedback on the neurofedora brochure within the next week -- Done (MeWjOr, 18:09:41) * https://pagure.io/design/issue/661 -> brochure ticket (FranciscoD, 18:10:15) * ACTION: everyone please take a look at the brochure and provide feedback: https://pagure.io/design/issue/661 (FranciscoD, 18:11:24) * lbazan to work on pending review tickets (MeWjOr, 18:13:38) * LINK: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&priority=0&assig… (FranciscoD, 18:14:56) * numpoly is in testing: https://bugzilla.redhat.com/show_bug.cgi?id=1808552 (FranciscoD, 18:15:32) * pydeps is also in testing: https://bugzilla.redhat.com/show_bug.cgi?id=1741624 (FranciscoD, 18:15:52) * Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… (MeWjOr, 18:16:57) * LINK: https://pagure.io/neuro-sig/NeuroFedora/issue/351 (FranciscoD, 18:18:32) * FranciscoD will write and publish a blog post to sync with F32 release: https://pagure.io/neuro-sig/NeuroFedora/issue/351 (FranciscoD, 18:18:44) * ACTION: FranciscoD share link to post here in the channel so we can spread it on our social media channels (FranciscoD, 18:19:46) * Bugzilla bugs: https://tinyurl.com/neurofedora-bugs (MeWjOr, 18:21:53) * LINK: https://bugzilla.redhat.com/buglist.cgi?classification=Fedora&component=pyt… (FranciscoD, 18:28:57) * LINK: https://paste.centos.org/view/d236c565 -> utils (FranciscoD, 18:35:58) * LINK: https://bugzilla.redhat.com/show_bug.cgi?id=1827957 + https://bugzilla.redhat.com/show_bug.cgi?id=1828079 (FranciscoD, 18:40:35) * FranciscoD needs two packages reviewed: https://bugzilla.redhat.com/show_bug.cgi?id=1828079 + https://bugzilla.redhat.com/show_bug.cgi?id=1827957 (FranciscoD, 18:40:58) * compose status (MeWjOr, 18:42:29) * ACTION: FranciscoD update docs to remove info about the iso image we generated (FranciscoD, 18:47:08) * rawhide compose will start functioning once this PR is merged and json pickle built: https://src.fedoraproject.org/rpms/python-jsonpickle/pull-request/4 (FranciscoD, 18:47:28) * MeWjOr will monitor composes until we find another spin master (FranciscoD, 18:48:08) * ACTION: FranciscoD e-mail devel list asking for volunteers (FranciscoD, 18:48:21) * ACTION: FranciscoD add spin-master to list of open positions in blog post (FranciscoD, 18:48:30) * ACTION: FranciscoD e-mail neuroscience mailing lists about the CompNeuro release (FranciscoD, 18:50:35) * neuroscience query of the week? (MeWjOr, 18:51:32) * https://pagure.io/neuro-sig/NeuroFedora/issue/318 (MeWjOr, 18:52:09) * open floor (MeWjOr, 18:59:36) Meeting ended at 19:03:45 UTC. Action Items ------------ * everyone please take a look at the brochure and provide feedback: https://pagure.io/design/issue/661 * FranciscoD share link to post here in the channel so we can spread it on our social media channels * FranciscoD update docs to remove info about the iso image we generated * FranciscoD e-mail devel list asking for volunteers * FranciscoD add spin-master to list of open positions in blog post * FranciscoD e-mail neuroscience mailing lists about the CompNeuro release Action Items, by person ----------------------- * FranciscoD * FranciscoD share link to post here in the channel so we can spread it on our social media channels * FranciscoD update docs to remove info about the iso image we generated * FranciscoD e-mail devel list asking for volunteers * FranciscoD add spin-master to list of open positions in blog post * FranciscoD e-mail neuroscience mailing lists about the CompNeuro release * **UNASSIGNED** * everyone please take a look at the brochure and provide feedback: https://pagure.io/design/issue/661 People Present (lines said) --------------------------- * FranciscoD (126) * MeWjOr (118) * zodbot (17) * mhough (6) * fm-neuro (6) * blackfile (1) * tg-fedneuro (1) * alciregi (0) * bt0 (0) * LoKoMurdoK (0) * gicmo (0) * zbyszek (0) Generated by `MeetBot`_ 0.1.4 .. _`MeetBot`: http://wiki.debian.org/MeetBot -- Thanks Regards Aniket Pradhan http://home.iiitd.edu.in/~aniket17133/ Aliases: MeWjOr/major () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments

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Open NeuroFedora Meeting: 1800 UTC on Monday, 27th April.
by Aniket Pradhan 26 Apr '20

26 Apr '20

Hey there! You are invited to attend the next Open NeuroFedora team meeting this week on Tuesday at 1600UTC in #fedora-neuro on IRC (Freenode): https://webchat.freenode.net/?channels=#fedora-neuro The channel is bridged to Telegram, so you can also join us there on the @NeuroFedora group: https://t.me/NeuroFedora You can convert the meeting time to your local time using this command in a terminal: $ date --date='TZ="UTC" 1800 next Mon' or using this link: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroFedora+Meeti… The meeting will be chaired by @major (that's me). The agenda for the meeting is: - Introductions and roll call. - Tasks from last week's meeting: https://meetbot.fedoraproject.org/fedora-neuro/2020-04-07/neurofedora.2020-… - Open Pagure tickets: https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=S%3A+Next+m… - Neuroscience query of the week. - Next meeting day, and chair. - Open floor. We hope to see you there! -- Thanks Regards Aniket Pradhan http://home.iiitd.edu.in/~aniket17133/ Aliases: MeWjOr/major () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments

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Fwd: [SPM] Call for applications: Neuromatch Summer Academy Students, TAs and Mentors
by Morgan Hough 21 Apr '20

21 Apr '20

---------- Forwarded message --------- From: Brad Wyble <bwyble(a)gmail.com> Date: Tue, Apr 21, 2020 at 8:41 AM Subject: [SPM] Call for applications: Neuromatch Summer Academy Students, TAs and Mentors To: <SPM(a)jiscmail.ac.uk> The pandemic has shut down nearly every summer program in the world at which students, postdocs and faculty would normally gather to acquire crucial skills and build networks. We’re building a program to replace this loss. Our plan is to have a 3-week online course July 13-31 focused on computational analysis and simulation of neural data with intensive mentoring by knowledgeable TAs and faculty mentors to help with projects. Tuition will be relatively minimal (~ 100-200 USD) and also voluntary. TAs will be paid a stipend for their time because it will be intensive. Mentorship by faculty will be substantially less work. Interested in signing up as a potential participant, a TA, or a faculty mentor? Fill out one of the three forms below. Also, please feel free to send this out as widely as possible. We’re trying to cast a global net, especially to people outside of the US and Europe. Tutorials will take place in parallel tracks in different time zones and in multiple languages when possible. Note that the deadline for applications is April 27. Webpage: https://neuromatch.io/academy/ Form for student applications https://docs.google.com/forms/d/e/1FAIpQLSen1oyFWIQ38vlBSxUdlWU4AwQ_UYGqQZc… Form for TA applications https://docs.google.com/forms/d/e/1FAIpQLSc4aL49WV_dnt7WlXjEwsY8Mb30I2E0VHa… Form for Mentor Applications https://docs.google.com/forms/d/e/1FAIpQLSef-slmLcnVT7H-wkM-7wT5ePBh3TVg7UX… -- Brad Wyble Associate Professor Psychology Department Penn State University http://wyblelab.com

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Next meeting: Date and Time.
by Aniket Pradhan 20 Apr '20

20 Apr '20

Hello all I just had a look at the results of the whenisgood that was passed last week. There was no slot that suited everyone who responded, so I selected the one so that most people in the group can make it. We can have our meeting on 27th April (Monday) at 1800 UTC. I hope that the attendees find the time/day suitable. I will be happy to chair the meeting, but if anyone else wants to do it, they are welcome to do so. -- Thanks Regards Aniket Pradhan http://home.iiitd.edu.in/~aniket17133/ Aliases: MeWjOr/major () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments

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Tutorial: analysing fMRI data with SPM
by Ankur Sinha 18 Apr '20

18 Apr '20

Hi! I ran into this SPM tutorial. It'll be useful for folks that are looking to learn how to analyse fMRI data: https://andysbrainbook.readthedocs.io/en/latest/SPM/SPM_Overview.html Quoting the introduction: "This course will show you how to analyze an fMRI dataset from start to finish. We will begin by downloading a sample dataset and inspecting the anatomical and functional images for each subject. We will then preprocess the data, which removes noise and enhances the signal in the images. Once the images have been preprocessed, we will create a model representing what we think the BOLD signal, a measure of neural activity, should look like in our images. During model fitting we compare this model with the signal in different areas of the image. This model fit is a measure of the strength of the signal under different conditions - for example, we can take the difference of the signal between conditions A and B of the experiment to see which condition leads to a larger BOLD response. Once a model has been created for each subject and the BOLD response has been estimated for each condition, we can do any kind of group analysis we like: Paired t-tests, between-group t-tests, interactions, and so on. The goal of this course is to calculate a simple within-subjects contrast between two conditions, and test whether it is significant across subjects. You will also learn how to create figures showing whole-brain analyses, similar to what you see published in the neuroimaging journals, and how to do a region of interest (ROI) analysis. This course is designed to build your confidence in working with fMRI data, increase your fluency with the basic terms of fMRI analysis, and help you make educated choices during each step. Some chapters have exercises to help you practice what you’ve learned and to prepare you for the next chapter. Once you have mastered the fundamentals of this course, you will be able to apply them to other datasets of your choosing." We do not yet have SPM packaged for Fedora, but it is on our list of packages: https://pagure.io/neuro-sig/NeuroFedora/issue/101 -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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neurord requires maven-release which has been orphaned
by Ankur Sinha 15 Apr '20

15 Apr '20

On Tue, Apr 14, 2020 11:06:27 +0200, Miro Hrončok wrote: > neuro-sig: maven-release, orangefs neurord requires maven-release. Should we take it up? https://churchyard.fedorapeople.org/orphans-2020-04-14.txt @zbyszek, what do you think? -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Reading material: The Neuroscientist, A Field Guide - The Spike - Medium
by Ankur Sinha 14 Apr '20

14 Apr '20

This is a good, fun read. It gives an idea of the different things that all come under the umbrella of neuroscience: https://medium.com/the-spike/the-neuroscientist-a-field-guide-ac15bb47372f (I'm a "computational neuroscientist") -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Choosing a suitable time for the next meeting.
by Aniket Pradhan 13 Apr '20

13 Apr '20

Hello there I have created a new whenisgood so that we can plan the time and the day for our next meeting. Please click on the following link and select your suitable time: http://whenisgood.net/neurofedora_meeting Make sure to select your timezone appropriately. We shall collect the results in next week and will meet at a suitable time. Please fill in your preference by this week. -- Thanks Regards Aniket Pradhan http://home.iiitd.edu.in/~aniket17133/ Aliases: MeWjOr/major () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments

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NeuroFedora brochure up for review.
by Aniket Pradhan 07 Apr '20

07 Apr '20

Hello people! The NeuroFedora brochure is coming around great and it would be wonderful if you all could spare some time and provide some feedback on it. You can have a look at the brochure here [0]. We have timeboxed the whole review to a week so that Smera can make the necessary changes and we can start using the brochure by then. [0]: https://pagure.io/neuro-sig/NeuroFedora/issue/301 -- Thanks Regards Aniket Pradhan http://home.iiitd.edu.in/~aniket17133/ Aliases: MeWjOr/major () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments

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Neurofedora April 2020